Table 1.
Expected and observed Cy5/Cy3 ratios for Arabidopsis spike controls in cDNA microarray hybridizations using five different labeling methods.
| Spikes | Expected ratio | Observed ratio for the five methods1: | Range3 of MMR values | ||||
| 1 | 2 | 3 | 4 | 5 | |||
| CyScribe [50 μg]2 | FairPlay [20 μg] | TSA [5 μg] | 3DNA [5 μg] | 3DNA50 [20 μg] | |||
| Spike 7 | 0.125 | 0.16 (0.05)4 | 0.17 (0.05) | 0.10 (0.04) | 0.10 (0.06) | 0.17 (0.04) | 0.10 – 0.17 |
| Spike 10 | 0.25 | 0.28 (0.09) | 0.44 (0.11) | 0.25 (0.11) | 0.26 (0.17) | 0.37 (0.10) | 0.25 – 0.44 |
| Spike 9 | 0.33 | 0.25 (0.08) | 0.49 (0.18) | 0.27 (0.11) | 0.22 (0.13) | 0.27 (0.10) | 0.22 – 0.49 |
| Spike 8 | 0.50 | 0.60 (0.21) | 0.67 (0.11) | 0.46 (0.14) | 0.45 (0.17) | 0.46 (0.11) | 0.45 – 0.67 |
| Spike 1 | 1.00 | 1.22 (0.41) | 1.72 (0.28) | 1.69 (0.69) | 1.64 (0.83) | 2.42 (0.65) | 1.22 – 2.42 |
| Spike 2 | 2.00 | 1.85 (0.70) | 2.66 (0.64) | 3.12 (1.20) | 2.40 (0.51) | 2.41 (0.53) | 1.85 – 2.41 |
| Spike 3 | 3.00 | 1.56 (0.60) | 3.58 (1.36) | 4.20 (1.90) | 3.85 (0.70) | 3.44 (0.79) | 1.56 – 4.20 |
| Spike 4 | 4.00 | 3.92 (1.34) | 4.85 (0.95) | 7.04 (2.77) | 5.15 (1.26) | 4.24 (1.06) | 3.92 – 7.04 |
| Spike 5 | 5.00 | 5.63 (1.80) | 7.22 (1.39) | 13.99 (6.56) | 7.66 (1.25) | 5.78 (1.45) | 5.63 – 13.99 |
| Spike 6 | 6.00 | 5.94 (2.04) | 7.97 (1.90) | 18.63 (10.64) | 5.38 (1.13) | 6.28 (1.16) | 5.38 – 18.63 |
1The observed ratio values for the first four protocols are median of medians of ratios (MMR) from four replicate hybridizations. For the 3DNA50 method, the data are based on three replicate hybridizations. 2μg total RNA used in labeling reactions. 3The range is given over MMR values for the five different methods. 4The between-array standard deviations, given in parenthesis, represent the standard deviation of the four (three) MMR values from the replicate hybridizations for each method.